[R] mb.long {timecourse}

[statfan]

How do you identify the genes which are differentially expressed using the
mb.long function?  More specifically, in the fruitfly example (see below),
we begin with an expression matrix containing 2000 genes.  How do I obtain
not only the proportion of differentially expressed genes, but also the
subset of genes which are differentially expressed?

data(fruitfly)
colnames(fruitfly) ## check if arrays are arranged in the default order
gnames <- rownames(fruitfly)
assay <- rep(c("A", "B", "C"), each = 12)
time.grp <- rep(c(1:12), 3)
size <- rep(3, nrow(fruitfly))

out1 <- mb.long(fruitfly, times=12, reps=size, rep.grp = assay, time.grp =
time.grp)
summary(out1)
plotProfile(out1, type="b", gnames=gnames, legloc=c(2,15),
pch=c("A","B","C"), xlab="Hour")

> summary(out1)
                Length Class  Mode   
M               72000  -none- numeric
prop                1  -none- numeric
nu                  1  -none- numeric
Lambda1           121  -none- numeric
percent             2  -none- numeric
size             2000  -none- numeric
con.group          36  -none- numeric
rep.group          36  -none- numeric
time.group         36  -none- numeric
HotellingT2      2000  -none- numeric
pos.HotellingT2  2000  -none- numeric

Thanks to anyone who can shed light on this matter.

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